Were all five types of beer line vinyl, or were any of them actual FDA (or it's AU counterpart) approved beverage line? The Tygon stuff I bought is lined and completely inert - the beer doesn't change after sitting in the line for an extended period of time. I have some cheap tubing that I use for blowoff and whatnot, and it goes from clear to opaque if it sits in StarSan too long (ie, one day). I've left the Tygon lines full of StarSan for a week and it doesn't discolor at all.
That's why I suggested better lines. It may very well be the chemical makeup of the beer, but it's easier (and healthier, imo) to change the lines to something inert, rather than trying completely redo your beer.